Determination of the clastogenic potential of new chemical entities, particularly pharmaceuticals, is an important part of the overall safety assessment of such drugs. It is appreciated that clastogenicity can arise from perturbation of many different cellular processes distinct from direct DNA/drug interactions. One such alternative clastogenic process is inhibition of DNA topoisomerase II, during which process the topoisomerase/DNA/drug ternary complex forms stable DNA double‐strand breaks (cleavable complex), which become templates for recombinational, mutagenic, and chromosomal fragmentation events. Without extensive experimentation, it is generally not possible to distinguish clastogenicity arising from direct drug/DNA interaction from that arising from inhibition of topoisomerase II. In the present investigation, we demonstrate that specific catalytic inhibitors of DNA topoisomerase II reduce the clastogenicity of topoisomerase poisons but not that arising via non‐topoisomerase‐dependent mechanisms. In particular, it is shown that catalytic topoisomerase II inhibitors such as chloroquine, sodium azide, and A‐74932, as well as certain intercalating agents such as 9‐aminoacridine and ethidium bromide, strongly antagonize the formation of micronuclei induced by the DNA gyrase inhibitor clinafloxacin and the antitumor topoisomerase II poison etoposide. These catalytic inhibitors are also shown to antagonize the clastogenicity of experimental compounds and novel pharmaceuticals presumed to be DNA intercalating agents by virtue of their response in a cell‐based bleomycin amplification assay. We extend our previous hypothesis, suggesting that the clastogenicity of some nonstructurally alerting drugs may be due to an as yet unappreciated propensity for DNA intercalation. It is further proposed that intercalation‐dependent inhibition of DNA topoisomerase II may be responsible for this clastogenicity and that this may be detected in intact mammalian cells with the use of catalytic topoisomerase inhibitors. Environ. Mol. Mutagen. 35:13–21, 2000 © 2000 Wiley‐Liss, Inc.